edgelist.py :  » Network » NetworkX » networkx-1.1 » networkx » readwrite » Python Open Source

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Python Open Source » Network » NetworkX 
NetworkX » networkx 1.1 » networkx » readwrite » edgelist.py
"""
**********
Edge Lists
**********

Read and write NetworkX graphs as edge lists.

You can read or write three formats of edge lists with these functions.

Node pairs::

 1 2 # no data

Dictionary as data::

 1 2 {'weight':7, 'color':'green'} 

Arbitrary data::

 1 2 7 green

See the read_edgelist() function for details and examples.

"""
__author__ = """Aric Hagberg (hagberg@lanl.gov)\nDan Schult (dschult@colgate.edu)"""
#    Copyright (C) 2004-2010 by 
#    Aric Hagberg <hagberg@lanl.gov>
#    Dan Schult <dschult@colgate.edu>
#    Pieter Swart <swart@lanl.gov>
#    All rights reserved.
#    BSD license.

__all__ = ['read_edgelist', 
           'write_edgelist',
           'read_weighted_edgelist',
           'write_weighted_edgelist'
           ]

from networkx.utils import is_string_like,_get_fh
import networkx as nx


def write_edgelist(G, path, comments="#", delimiter=' ', data=True):
    """Write graph as a list of edges.

    Parameters
    ----------
    G : graph
       A NetworkX graph
    path : file or string
       File or filename to write.  
       Filenames ending in .gz or .bz2 will be compressed.
    comments : string, optional
       The character used to indicate the start of a comment 
    delimiter : string, optional
       The string used to separate values.  The default is whitespace.
    data : bool or list, optional
       If False write no edge data.
       If True write a string representation of the edge data dictionary..  
       If a list (or other iterable) is provided, write the  keys specified 
       in the list.

    Examples
    --------
    >>> G=nx.path_graph(4)
    >>> nx.write_edgelist(G, "test.edgelist")
    >>> G=nx.path_graph(4)
    >>> fh=open("test.edgelist",'w')
    >>> nx.write_edgelist(G, fh)
    >>> nx.write_edgelist(G, "test.edgelist.gz")
    >>> nx.write_edgelist(G, "test.edgelist.gz", data=False)

    >>> import sys
    >>> G=nx.Graph()
    >>> G.add_edge(1,2,weight=7,color='red')
    >>> nx.write_edgelist(G,sys.stdout,data=False)
    1 2
    >>> nx.write_edgelist(G,sys.stdout,data=['color'])
    1 2 red
    >>> nx.write_edgelist(G,sys.stdout,data=['color','weight'])
    1 2 red 7
    
    Notes
    -----
    The file will use the default text encoding on your system.
    It is possible to write files in other encodings by opening
    the file with the codecs module.  See doc/examples/unicode.py
    for hints.

    See Also
    --------
    write_edgelist()
    write_weighted_edgelist()
    """
    fh=_get_fh(path,mode='w')

    def make_str(t):
        if is_string_like(t): return t
        return str(t)

    if data is True or data is False:
        for e in G.edges(data=data):
            fh.write(delimiter.join(map(make_str,e))+"\n")
    else:
        for u,v,d in G.edges(data=True):
            e=[u,v]
            e.extend(d[k] for k in data)
            fh.write(delimiter.join(map(make_str,e))+"\n")


def read_edgelist(path, 
                  comments="#", 
                  delimiter=' ',
                  create_using=None, 
                  nodetype=None, 
                  data=True,
                  edgetype=None,
                  ):
    """Read a graph from a list of edges.

    Parameters
    ----------
    path : file or string
       File or filename to write.  
       Filenames ending in .gz or .bz2 will be uncompressed.
    comments : string, optional
       The character used to indicate the start of a comment. 
    delimiter : string, optional
       The string used to separate values.  The default is whitespace.
    create_using : Graph container, optional, 
       Use specified container to build graph.  The default is networkx.Graph,
       an undirected graph.
    nodetype : int, float, str, Python type, optional
       Convert node data from strings to specified type
    data : list of (label,type) tuples
       Tuples specifying dictionary key names and types for edge data
    edgetype : int, float, str, Python type, optional OBSOLETE
       Convert edge data from strings to specified type and use as 'weight'

    Returns
    -------
    G : graph
       A networkx Graph or other type specified with create_using

    Examples
    --------
    >>> nx.write_edgelist(nx.path_graph(4), "test.edgelist")
    >>> G=nx.read_edgelist("test.edgelist")

    >>> fh=open("test.edgelist")
    >>> G=nx.read_edgelist(fh)

    >>> G=nx.read_edgelist("test.edgelist", nodetype=int)
    >>> G=nx.read_edgelist("test.edgelist",create_using=nx.DiGraph())

    Notes
    -----
    Since nodes must be hashable, the function nodetype must return hashable
    types (e.g. int, float, str, frozenset - or tuples of those, etc.) 

    Example edgelist file formats.

    Without edge data::

     # read with 
     # >>> G=nx.read_edgelist(fh,data=False)
     # source target
     a b
     a c
     d e

    With edge data as dictionary:: 

     # read with 
     # >>> G=nx.read_edgelist(fh,data=True)
     # source target data  
     a b {'weight': 1}
     a c {'weight': 3.14159}
     d e {'fruit': 'apple'}

    With arbitrary edge data:: 

     # read with 
     # >>> G=nx.read_edgelist(fh,data=[('weight',float')])
     # or
     # >>> G=nx.read_weighted_edgelist(fh)
     # source target data  
     a b 1
     a c 3.14159
     d e 42
    """
    if edgetype is not None: 
        import warnings
        warnings.warn('edgetype option is deprecated, use read_weighted_edgelist()', 
                      DeprecationWarning)
        return read_edgelist(path,
                             comments=comments,
                             delimiter=delimiter,
                             create_using=create_using,
                             nodetype=nodetype,
                             data=(('weight',edgetype),)
                             )
    try:
        from ast import literal_eval
    except:
        literal_eval=eval # use potentially unsafe built-in eval 
    if create_using is None:
        G=nx.Graph()
    else:
        try:
            G=create_using
            G.clear()
        except:
            raise TypeError("Input graph is not a NetworkX graph type")

    fh=_get_fh(path)

    for line in fh.readlines():
        p=line.find(comments)
        if p>=0:
            line = line[:line.find(comments)]
        if not len(line): continue
        # split line, should have 2 or more
        s=line.strip().split(delimiter)
        if len(s)<2: continue
        u=s.pop(0)
        v=s.pop(0)
        d=s
        if nodetype is not None:
            try:
                u=nodetype(u)
                v=nodetype(v)
            except:
                raise TypeError("Failed to convert nodes %s,%s to type %s."\
                          %(u,v,nodetype))

        if len(d)==0 or data is False:
            # no data or data type specified
            edgedata={}
        elif data is True:
            # no edge types specified
            try: # try to evaluate as dictionary
                edgedata=dict(literal_eval(' '.join(d)))
            except:
                raise TypeError("Failed to convert edge data (%s) to dictionary."%(d))
        else:
            # convert edge data to dictionary with specified keys and type
            if len(d)!=len(data):
                raise IndexError("Edge data %s and data_keys %s are not the same length"%
                                 (d, data))
            edgedata={}
            for (edge_key,edge_type),edge_value in zip(data,d):
                try:
                    edge_value=edge_type(edge_value)
                except:
                    raise TypeError("Failed to convert edge data (%s) to type %s."%
                                    (edge_key, edge_type))
                edgedata.update({edge_key:edge_value})
        G.add_edge(u,v,**edgedata)  
    return G


def write_weighted_edgelist(G, path, 
                            comments="#", 
                            delimiter=' '):
    """Write graph G as a list of edges with numeric weights.

    Parameters
    ----------
    G : graph
       A NetworkX graph
    path : file or string
       File or filename to write.  
       Filenames ending in .gz or .bz2 will be compressed.
    comments : string, optional
       The character used to indicate the start of a comment 
    delimiter : string, optional
       The string used to separate values.  The default is whitespace.

    Examples
    --------
    >>> import sys
    >>> G=nx.Graph()
    >>> G.add_edge(1,2,weight=7)
    >>> nx.write_weighted_edgelist(G,sys.stdout)
    1 2 7

    See Also
    --------
    read_edgelist()
    write_edgelist()
    write_weighted_edgelist()

"""
    write_edgelist(G,path,
                   comments=comments,
                   delimiter=delimiter,
                   data=('weight',))
    
def read_weighted_edgelist(path, comments="#", delimiter=' ',
                           create_using=None, nodetype=None) :

    """Read list of edges with numeric weights.

    Parameters
    ----------
    path : file or string
       File or filename to write.  
       Filenames ending in .gz or .bz2 will be uncompressed.
    comments : string, optional
       The character used to indicate the start of a comment. 
    delimiter : string, optional
       The string used to separate values.  The default is whitespace.
    create_using : Graph container, optional, 
       Use specified container to build graph.  The default is networkx.Graph,
       an undirected graph.
    nodetype : int, float, str, Python type, optional
       Convert node data from strings to specified type

    Returns
    -------
    G : graph
       A networkx Graph or other type specified with create_using

    Notes
    -----
    Since nodes must be hashable, the function nodetype must return hashable
    types (e.g. int, float, str, frozenset - or tuples of those, etc.) 

    Example edgelist file format.

    With numeric edge data:: 

     # read with 
     # >>> G=nx.read_weighted_edgelist(fh)
     # source target data  
     a b 1
     a c 3.14159
     d e 42
    """
    return read_edgelist(path,
                         comments=comments,
                         delimiter=delimiter,
                         create_using=create_using,
                         nodetype=nodetype,
                         data=(('weight',float),)
                         )
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